Linda,
As I've just started doing DNA fragment analysis in our new core, my
experience is limited, but I can tell you how we're presently carrying out
a whole-genome scan using a mouse marker set from Research Genetics. The
choice was easy for me as I'm only looking at 12 mouse DNAs, but scanning
their genomes using ~420 markers (dinucleotide-repeated microsatellites).
Therefore, each row (A-H) of 12 wells is identical wrt the template DNAs
plated in them, and I PCR 8 markers per 96-well plate. The down side?
Eight PCR master mixes per plate. I avoid potential problems with
artifacts in the PCRs derived from the master mixes prepped first by using
antibody-mediated "hot start" PCR - enabling me to set up PCR at room
temperature and with lessened time constraints to get my reactions in the
thermalcycler in minutes. We've PCR'ed about a third of the marker set so
far with good results. Demand for fragment analysis here has not (yet)
reached a level where I'm considering using 384-well plates.
Bob
At 04:47 PM 10/30/2000 -0700, you wrote:
>Here are a couple of questions for genotyping labs:
>
>When you are doing a Genome Scan with a large marker set, does anyone set up
>their PCR trays with multiple markers and a single DNA or does everyone use
>multiple DNAs and a single marker per tray?
>
>What about 384-well trays? Does everyone treat them as if they were 4
>96-well trays (i.e. A1, A2, B1, B2 quadrants spaced the same as 96-wells) or
>does anyone treat them differently?
>
>Linda
>
>Linda Wood Ballard
>Genomics Core Facility
>University of Utah
>50 N. Medical Dr. 4A430A SOM
>Salt Lake City, UT 84132
Robert G. Keefe, Ph.D.
Wadsworth Center/NYS Dept. of Health
Genomics Core Facility
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